You're right, technically for print it's a better practice to change the color of the element than transparency in most case, unless the transparency adds something to the design. But that is if you like to be certain of the color you'll get once your file will be printed. For web, it matters less.
The reason why designers often prefer to use transparency is because it's easier for them to improvise with their design and play around until they get the "desired" effect. Since Adobe fully released the transparency effects in vector and when InDesign came out, it almost became a way to create.
It's possible that some designers who have prepress experience from the early 2000 will prefer the control of using the exact color instead of transparency because of the full control on the results (and reliability of this method*) while the designers who started learning graphic design with Illustrator 10, Photoshop or InDesign (or embraced it) will prefer using transparency for practical reasons. Sometimes, designers will do their designs with transparency during the creation process and then convert some transparency in their design to exact colors.
In both case it's really a question of preference, "comfort" and priorities.
*and because they lost half their hair and sanity "ripping" the new InDesign files full of transparency when it came out